Graph theoretical analysis of the phytosociological structure of plant communities: An application to mixed forest

Summary A sampling method, compatible with the theory elaborated in the previous paper, was used to investigate the mixed-forest community of a woodlot in Southern Ontario. The results provide an illustration of the graph theoretical methods developed for the elucidation of a community's phytosociological structure. Certain conjectures about the community are tested and it is found that Goodall's hypothesis concerning the nature of a plant community is supported. The tests also show that the vegetation of the study area forms a single natural grouping despite the disparity of the position ofAcer saccharum and the polarity evident among the other tree species.Nomenclature follows Gleason (1952).From a thesis submitted to the University of Toronto in partial fulfilment of the requirements for the degree of Master of Science.I wish to thank Dr. G. A. Yarranton for his ideas and helpful supervision, and my father for his advice and encouragement. Thanks ag also due to Miss J. E. Ellard and Mr. S. Roy who helped prepare the figures. This research has been supported by a National Research Council of Canada and by NRCC grant A-2910.     

Graph theoretical methods for comparing phytosociological structures

This paper describes some methods that can be used to compare the phytosociological structure of plant communities using some graph theoretic properties of the directed graphs that represent them. In such a graph, the species are represented by points and the association of species A with species B is represented by a directed line segment going from B to A. Two communities can be compared using simple indices to measure the similarity of their species-lists (point similarity) and of the species associations in them (line similarity). A more sophisticated and informative measure of line similarity is the probability that, given the number of points shared by two graphs, they have at least as many lines in common as they are observed to have. A formula for calculating that probability is given here. The graphs of community structure can also be compared with respect to the homogeneity of the distribution of the lines among the points, a property related to the number of species that are important in determining the composition of the community. These techniques are illustrated using the graphs of the phytosociological structure of intertidal seaweed communities on the southeast coast of Nova Scotia.Nomenclature follows: South and Cardinal (1970)     

Phytomass structure of natural plant communities on spodosols in southern Venezuela: the Bana woodland

Bana, or Low Amazon Caatinga is an evergreen sclerophyllous woodland. It occurs on bleached quartz sands in the lowlands of SW Venezuela, where it occupies relatively small ‘islands’ amidst Tall Amazon Caatinga which is exclusively developed on tropaquods. There is an outer vegetation belt about 20 m in width in which trees over 10 m in height occur (Tall Bana); its structure and floristic composition resemble Tall Amazon Caatinga. Low Bana (maximum tree height usually below 5 m) follows next. The central part is occupied by Open Bana in which even lower trees are very widely spaced. Destructive phytomass sampling was carried out for chemical analyses in seven plots along a 150 m line across the zonation. The total dry matter of living plants including roots of Tall Bana (30–32 kg/m²) compares rather well with 41 kg/m² in Tall Amazon Caatinga. This is only 9–14 kg/m² in Low Bana, and 4–6 kg/m² in Open Bana. The average root % of total phytomass increases from 41% in Tall Bana to 63% in Low Bana, and is 88% in Open Bana. Average total dry dead above-ground phytomass (including standing trees and stumps) declines from 1 kg/m² in Tall Bana to 0.2 kg/m² in Open Bana. An accumulation of dead matter in Low and Open Bana, relative to the above-ground phytomass of living plants, is noted and this contrasts with the general absence of raw humus in the soil. Eighty-two species of woody plants (dbh≥1 cm) were recorded on the total plot area (640 m²); 90% of the species are also known to occur in Tall Amazon Caatinga. The species number declines from 59 in Tall Bana to 18 in Open Bana. Mesophylls sensu strictu dominate in Tall Bana, while notophylls are dominant in Low and Open Bana. Herbaceous species are less numerous: most of them belong to the Araceae, Bromeliaceae, Orchidaceae, Droseraceae, Eriocaulaceae and Xyridaceae.     

The influence of coastal upwelling on the functional structure of rocky intertidal communities

Summary Relationships between organisms at all trophic levels are influenced by the primary productivity of the ecosystem, and factors which enhance rates of primary production may modify trophic relationships and community structure. Nutrient enrichment of intertidal and nearshore waters leads to enhanced production by intertidal algae, and it was hypothesized that where rocky shores are washed by nutrient-rich upwelled waters, the intertidal communities should show a characteristic functional structure, based on the effects of enhanced primary production. Study sites were chosen on rocky shores in southern Africa, central Chile and the Canary Islands, in areas with and without coastal upwelling, and mid-shore community structure at these sites was analysed in terms of the abundance of certain functional guilds of organisms.It was found that algal cover and the biomass of herbivorous limpets supported per unit area on rocky shores were significantly greater in regions of coastal upwelling than in regions where upwelling did not occur. Ground cover by sessile filter-feeding organisms was significantly greater on shores in non-upwelled areas. However, correspondence analysis showed no functional aspect of intertidal community structure that was characteristic of coasts washed by upwelled waters. Primary reasons for this are probably the large variations in the nature of nutrient enrichment that accompanies upwelling, and in the nutrient status of non-upwelled areas. Other factors are man's exploitation of intertidal organisms and differences in the genetic origins of the intertidal species involved.     

The influence of anthropogenic disturbances on the structure of arboreal arthropod communities

In the framework of our research, aimed at understanding the processes structuring tropical arthropod communities, we investigated the changes occurring in tree crown communities of forests of different disturbance levels. These were a mixed dipterocarp primary lowland rain forest in Kinabalu National Park (in Sabah, Malaysia) and, some kilometres away, three forests of regeneration periods 5, 15, and 40 years following a clear-cut. These disturbed forest sites were adjacent to one another and merged into mature forest. From each forest at least ten individuals of one tree species were sampled using the fogging method. In the primary forest relative proportions of some arthropod taxa differed on the ordinal and familial level significantly within trees. The dominance of Formicidae was characteristic as was the almost complete lack of less mobile arthropods such as Lepidoptera larvae. In the five-year- old forest, differences in relative proportions among most taxa had almost disappeared. Formicidae abundances had declined drastically which coincided with an increase of Lepidoptera larvae. With progressing forest succession, arthropod communities increasingly converged on the pattern of primary forest, and total ant abundance as well as diversity increased significantly. Ant communities in the most disturbed forest were of low structural complexity, and to a large degree predictable in species arrangement, but became more and more unpredictable as the complexity of the forest increased. Several species of Coleoptera and non-formicine Hymenoptera occurred in high numbers in the youngest forest, contrasting with the mature forest where all species were typically rare. These changes may indicate a change in the structuring mechanisms from predominantly deterministic processes in disturbed forests to stochastic processes in mature forest.     

Plant traits,species pools and the prediction of relative abundance in plant communities: a maximum entropy approach

Questions: To what extent can Shipley et al.'s original maximum entropy model of trait‐based community assembly predict relative abundances of species over a large (3000 km²) landscape? How does variation in the species pool affect predictive ability of the model? How might the effects of missing traits be detected? How can non‐trait‐based processes be incorporated into the model? Location: Central England. Material and Methods: Using 10 traits measured on 506 plant species from 1308 1‐m² plots collected over 3000 km² in central England, we tested one aspect of Shipley et al.'s original maximum entropy model of “pure” trait‐based community assembly (S₁), and modified it to represent both a neutral (S₂) and a hybrid (S₃) scenario of community assembly at the local level. Predictive ability of the three corresponding models was determined with different species pool sizes (30, 60, 100 and 506 species). Statistical significance was tested using a distribution‐free permutation test. Results: Predictive ability was high and significantly different from random expectations in S₁. Predictive ability was low but significant in S₂. Highest predictive ability occurred when both neutral and trait‐based processes were included in the model (S₃). Increasing the pool size decreased predictive ability, but less so in S₃. Incorporating habitat affinity (to indicate missing traits) increased predictive ability. Conclusions: The measured functional traits were significantly related to species relative abundance. Our results both confirm the generality of the original model but also highlight the importance of (i) taking into account neutral processes during assembly of a plant community, and (ii) properly defining the species pool.     

The use of gene probes in the rapid analysis of natural microbial communities

Summary Hybridization probes produced from DNA sequences have proven to be a powerful tool in the rapid and sensitive analysis of natural microbial communities. By using function-specific probes, such as those identifying genes coding for photosynthesis, the potential a microbial community has for performing a given function may be rapidly determined. Gene probes have also been used in the identification and isolation of a specific catabolic genotype in less than one-fourth the time required for the conventional culture enrichment technique. Species-specific probes constructed from portions of genes coding for ribosomal RNA have been used for the rapid identification and enumeration of bacterial species in environmental samples. The use of reassociation kinetics as a measure of community diversity and complexity is also discussed. The successful application of this technique to community analysis may reduce the time required from 1 year, for conventional analysis, to 2 weeks.     

The role of seed traits in determining the phylogenetic structure of temperate plant communities

Background and Aims

Phylogenetic clustering of species within plant communities can be expected to result from environmental filtering acting on an evolutionary-conserved plant trait. One such a candidate trait is the embryo to seed-size ratio (E:S). A high E:S may allow faster germination immediately after imbibition, and is therefore assumed to be advantageous in dry habitats. In this study the hypothesis was tested that habitat filtering driven by soil moisture conditions and acting on seed germination and seedling establishment is an important ecological mechanism in structuring temperate plant communities.

Methods

Vegetation samplings were performed in three habitats located within 200 km of each other in western Europe: Ellenberg indicator values showed that the habitats selected differed substantially in terms of soil moisture and light availability. E.S ratio and seed mass data for all genera were obtained from literature. Data were analysed using recently developed phylogenetic methods.

Key Results

Genera with a similar E:S tend to co-occur, as low and high E:S genera dominate in moist and dry habitats, respectively. A phylogenetically clustered pattern of community structure was evident, and dispersion of E:S was positively related to phylogenetic dispersion.

Conclusions

The phenotypically and phylogenetically clustered pattern indicates that E:S-mediated habitat filtering is an important assembly process structuring the plant community of the temperate climate habitats studied.     

The controlled assembly of microcosmic communities: the selective extinction hypothesis

Summary Forty communities were assembled through the controlled inoculation of algae, protozoans and a rotifer according to either of 2 distinct introduction schedules. These introduction schedules were constructed such that species reinvaded on average either every 6 or 8 w. Ten of the 20 beakers experiencing each invasion schedule contained 300 ml of media; the remaining beakers in each invasion category contained 100 ml of media. Species richness consistently increased throughout the initial 4 w and 7 w of the experiment for the low and high invasion rate beakers, respectively. The numbers of species in the low rate beakers were uncorrelated with time during the last half of the experiment; however, species richness gradually declined during this period in the high rate beakers. The extinction rate is shown to be disproportionately higher for large organisms in the small microcosms. Such selective extinction is consistent with the MacArthur-Wilson equilibrium model.     

The effects of trophic structure and soil fertility on the assembly of plant communities: a microcosm experiment

Using closed, ventilated outdoor microcosms, plant communities were allowed to assemble from a pool of 48 herbaceous species comprising a wide range of plant functional types. The experiment involved factorial manipulation of soil fertility, invertebrate herbivores (slugs, grass aphids) and their predators (ground beetles, ladybirds). In the absence of herbivores the vegetation on soils of high, moderate and low fertility was dominated by plant species which under natural field conditions are restricted to fertile soils. At high fertility, the rate of competitive exclusion was rapid compared with communities persisting at lower fertility which remained species‐rich with high densities of individuals.
The effects of herbivory were profound and attributable mainly to the slug Deroceras reticulatum. At moderate and low soil fertility the main effect of herbivores was to change the ranking of plant species; palatable grasses (e.g. Poa annua, Poa trivialis and Lolium perenne) were suppressed and plant species of slower growth rate (e.g. Festuca rubra, Anthoxanthum odoratum, Festuca ovina) were promoted. More subtle impacts of herbivory altered the size structure of plant populations suggesting the preference, by slugs, for seedlings and small (suppressed) plants. Although ladybirds and their larvae persisted in low numbers in some microcosms, carnivory was more strongly in evidence (lower densities of D. reticulatum and reduced consumption of lettuce discs) in relation to the activities of the ground beetle Pterostichus melanarius. Only in the low fertility treatment, however, was this potential translated into effects on vegetation; for several plant species the frequency of large individuals increased in the presence of P. melanarius.
We conclude that outdoor microcosms provide a valuable ecological tool and, in particular, allow investigation of (a) the role of herbivores in promoting slow‐growing plant species in the vegetation of infertile habitats and (b) the protection of palatable plants against herbivores by carnivores.     

Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: Application to the lac repressor headpiece

Summary A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch of mathematics known as graph theory to identify prescribed NOE connectivity patterns characteristic of the regular secondary structures. Resonance assignment is achieved by connecting these patterns of secondary structure together, thereby matching the connected spin systems to specific segments of the protein sequence. The method known as SERENDIPITY refers to a set of routines developed in a modular fashion, where each program has one or several well-defined tasks. NOE templates for several secondary structure motifs have been developed and the method has been successfully applied to data obtained from NOESY-type spectra. The present report describes the application of the SERENDIPITY protocol to a 3D NOESY-HMQC spectrum of the ¹⁵N-labelled lac repressor headpiece protein. The application demonstrates that, under favourable conditions, fully automated identification of secondary structures and semi-automated assignment are feasible.Abbreviations 2D, 3D two-, three-dimensional - NOESY nuclear Overhauser enhancement spectroscopy - HMQC heteronuclear multiple quantum coherence - SSE secondary structure element - SERENDIPITY SEcondary structuRE ideNtification in multiDImensional ProteIn specTra analYsis Supplementary Material available from the authors: Two tables containing the total number of mappings resulting from the graph search procedure for simulated and experimental NOE data.     

3-Silaoxetane and 3-silathietane: structure and reactivity studies on the basis of spectroscopic data and theoretical calculations

The ab initio and DFT calculations (structural parameters, electron localization function (ELF)) on 3-silaoxetane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-oxa-3-silacyclobutane (1) and 3-silathietane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-sila-3-thiacyclobutane (2) show the cyclobutane ring in 2 as being non-planar with a C-Si-C angle of 89.2° and a C-S-C angle of 93.3°, whereas the cyclobutane ring in 1 is planar with an unusual small bond angle at the silicon atom of 74.7°, which can only be explained by bent bonds. Since the synthesis was performed in water, small bent angles cannot be indicative for high reactivity. The Raman spectra of 1 and 2 were then recorded and analyzed in the 1800-200 cm⁻¹ spectral region at various temperatures (300-10 K) with the help of the DFT calculation results (harmonic vibrational wavenumbers, Raman scattering activities). Although the wavenumber shifts are quite small, the subtle changes in the spectral features of the 3-silaoxetane and phenyl rings vibrational modes may indicate a loss of symmetry in 1 (between 200 and 150 K) and a possible phase transition in 2 (at about 200 K). Furthermore, the Raman spectra of 1 and 2 confirmed the ELF calculation results, excluding any bond interaction between the silicon and the oxygen or sulfur atom.     

Recovery without resilience: persistent disturbance and long-term shifts in the structure of fish and coral communities at Tiahura Reef, Moorea

Disturbances have a critical effect on the structure of natural communities. In this study long-term changes were examined in the reef community at Tiahura Reef, on the northern coast of Moorea, which had been subject to many and varied disturbances over the last 25 years. Tiahura Reef was subject to an outbreak of crown-of-thorns starfish (Acanthaster planci) in 1980–1981, causing significant declines in the abundance of scleractinian corals and butterflyfishes. By 2003, the abundance of corals and butterflyfishes had returned to former levels, but despite this apparent recovery, the species composition of coral communities and butterflyfish assemblages was very different from those recorded in 1979. Ongoing disturbances (including further outbreaks of crown-of-thorns starfish, cyclones, and coral bleaching events) appear to have prevented recovery of many important coral species (notably, Acropora spp.), which has had subsequent effects on the community structure of coral-feeding butterflyfishes. This study shows that recurrent disturbances may have persistent effects on the structure and dynamics of natural communities.     

Multivariate analysis of plant communities in the Narok district, Kenya: The influence of environmental factors and human disturbance

Species type in 42 samples was examined using ordination analysis to establish whether the vegetation pattern displays gradation due to environmental factors, and whether the pattern was being altered by human disturbance. The analysis displayed two patterns. First, the ordination on axis 1 demonstrated vegetation gradation from xeric communities on the plains to humid forests on the highland. This pattern is explained on the basis of moisture and nutrient variations. Vegetation vectors based on species presence-absence were correlated with average rainfall, carbon, nitrogen and zinc.The second was separation of disturbed and undisturbed forest and bushland site categories on axis 2 of the ordination space. This pattern suggests that disturbance response is interactive with moisture so that only in moist communities does a significant vegetation response to disturbance occur.     

Crystal structure analysis of a pentameric fungal and an icosahedral plant lumazine synthase reveals the structural basis for differences in assembly

Lumazine synthase catalyzes the penultimate step in the synthesis of riboflavin in plants, fungi, and microorganisms. The enzyme displays two quaternary structures, the pentameric forms in yeast and fungi and the 60-meric icosahedral capsids in plants and bacteria. To elucidate the structural features that might be responsible for differences in assembly, we have determined the crystal structures of lumazine synthase, complexed with the inhibitor 5-nitroso-6-ribitylamino-2,4-pyrimidinedione, from spinach and the fungus Magnaporthe grisea to 3.3 and 3.1 A resolution, respectively. The overall structure of the subunit and the mode of inhibitor binding are very similar in these enzyme species. The core of the subunit consists of a four-stranded parallel beta-sheet sandwiched between two helices on one side and three helices on the other. The packing of the five subunits in the pentameric M. grisea lumazine synthase is very similar to the packing in the pentameric substructures in the icosahedral capsid of the plant enzyme. Two structural features can be correlated to the differences in assembly. In the plant enzyme, the N-terminal beta-strand interacts with the beta-sheet of the adjacent subunit, thus extending the sheet from four to five strands. In fungal lumazine synthase, an insertion of two residues after strand beta1 results in a completely different orientation of this part of the polypeptide chain and this conformational difference prevents proper packing of the subunits at the trimer interface in the icosahedron. In the spinach enzyme, the beta-hairpin connecting helices alpha4 and alpha5 participates in the packing at the trimer interface of the icosahedron. Another insertion of two residues at this position of the polypeptide chain in the fungal enzyme disrupts the hydrogen bonding in the hairpin, and the resulting change in conformation of this loop also interferes with proper intrasubunit contacts at the trimer interface.     

Hypothesis/review: The structural basis of sweetness perception of sweet-tasting plant proteins can be deduced from sequence analysis

Human perception of sweetness, behind the felt pleasure, is thought to play a role as an indicator of energy density of foods. For humans, only a small number of plant proteins taste sweet. As non-caloric sweeteners, these plant proteins have attracted attention as candidates for the control of obesity, oral health and diabetic management. Significant advances have been made in the characterization of the sweet-tasting plant proteins, as well as their binding interactions with the appropriate receptors. The elucidation of sweet-taste receptor gene sequences represents an important step towards the understanding of sweet taste perception. However, many questions on the molecular basis of sweet-taste elicitation by plant proteins remain unanswered. In particular, why homologues of these proteins do not elicit similar responses? This question is discussed in this report, on the basis of available sequences and structures of sweet-tasting proteins, as well as of sweetness-sensing receptors. A simple procedure based on sequence comparisons between sweet-tasting protein and its homologous counterparts was proposed to identify critical residues for sweetness elicitation. The open question on the physiological function of sweet-tasting plant proteins is also considered. In particular, this review leads us to suggest that sweet-tasting proteins may interact with taste receptor in a serendipity manner.     

The effect of patch disturbance on stream invertebrate community structure: the influence of disturbance history

The effect of disturbance history on the recovery of benthic invertebrate communities following disturbance was investigated in four streams in the Southern Alps of New Zealand. Two of the streams had a history of fluctuating discharge and temperature while the others did not. Recovery from disturbance was tested experimentally using baskets of cobbles, a third of which were disturbed every week for 9 weeks, a further third every 3 weeks and the final third left undisturbed. Algal biiomass, number of invertebrate taxa and total number of invertebrates all declined in baskets disturbed more frequently. Although the relative abundance of some taxa declined with time since the last disturbance, no taxa showed a significant decline in absolute abundance. However, several taxa showed marked increases in relative abundance in the less disturbed treatments particularly at the more stable sites. In contrast to the predictions of ecological theory, numbers of taxa and total invertebrates appeared to recover more quickly in the more complex communities at the stable sites. However, if these communities are considered to represent only stable communities, they do support the view that more complex communities will be more resilient. Community structure at the stable sites was also more similar between baskets in the undisturbed treatment than at the unstable sites, suggesting communities had reached a constant state more quickly. The more rapid recovery of communities measured at the stable sites may have been a consequence of experimental scale; disturbed patches were only 0.045 m² in area and the higher densities of invertebrates at the stable sites meant a larger pool of colonists was available following each experimental disturbance. Nevertheless, ideas of stability in ecological theory and the scale of most spate events suggest this is the appropriate scale for examining community recovery. Furthermore, the larger pool of available colonists could not explain all the differences in community response, as patterns of change in community structure at the stable sites differed considerably more from those expected by purely random colonisation processes than at the unstable sites.